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- PDB-6pc4: Tubulin-RB3_SLD-TTL in complex with compound ABI-274 -

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Basic information

Entry
Database: PDB / ID: 6pc4
TitleTubulin-RB3_SLD-TTL in complex with compound ABI-274
Components
  • Stathmin-4
  • Tubulin Tyrosine Ligase
  • Tubulin alpha-1B chain
  • Tubulin beta-2B chain
KeywordsCELL CYCLE / Microtubule Inhibitor / Colchicine / Cancer
Function / homology
Function and homology information


tubulin-tyrosine ligase activity / Microtubule-dependent trafficking of connexons from Golgi to the plasma membrane / Hedgehog 'off' state / Cilium Assembly / Intraflagellar transport / COPI-dependent Golgi-to-ER retrograde traffic / Carboxyterminal post-translational modifications of tubulin / RHOH GTPase cycle / Sealing of the nuclear envelope (NE) by ESCRT-III / Kinesins ...tubulin-tyrosine ligase activity / Microtubule-dependent trafficking of connexons from Golgi to the plasma membrane / Hedgehog 'off' state / Cilium Assembly / Intraflagellar transport / COPI-dependent Golgi-to-ER retrograde traffic / Carboxyterminal post-translational modifications of tubulin / RHOH GTPase cycle / Sealing of the nuclear envelope (NE) by ESCRT-III / Kinesins / PKR-mediated signaling / The role of GTSE1 in G2/M progression after G2 checkpoint / Aggrephagy / Resolution of Sister Chromatid Cohesion / Mitotic Prometaphase / EML4 and NUDC in mitotic spindle formation / Separation of Sister Chromatids / RHO GTPases activate IQGAPs / RHO GTPases Activate Formins / Recruitment of NuMA to mitotic centrosomes / HSP90 chaperone cycle for steroid hormone receptors (SHR) in the presence of ligand / MHC class II antigen presentation / microtubule depolymerization / COPI-mediated anterograde transport / regulation of microtubule polymerization or depolymerization / tubulin binding / spindle microtubule / Hydrolases; Acting on acid anhydrides; Acting on GTP to facilitate cellular and subcellular movement / protein modification process / structural constituent of cytoskeleton / microtubule cytoskeleton organization / microtubule cytoskeleton / neuron projection development / mitotic cell cycle / growth cone / microtubule / neuron projection / nucleotide binding / GTPase activity / GTP binding / Golgi apparatus / metal ion binding / cytoplasm
Similarity search - Function
Methane Monooxygenase Hydroxylase; Chain G, domain 1 - #30 / Methane Monooxygenase Hydroxylase; Chain G, domain 1 / Helix hairpin bin / Tubulin/FtsZ, C-terminal domain / Tubulin/FtsZ, GTPase domain / Tubulin-tyrosine ligase/Tubulin polyglutamylase / Tubulin-tyrosine ligase family / TTL domain profile. / Stathmin family / Stathmin, conserved site ...Methane Monooxygenase Hydroxylase; Chain G, domain 1 - #30 / Methane Monooxygenase Hydroxylase; Chain G, domain 1 / Helix hairpin bin / Tubulin/FtsZ, C-terminal domain / Tubulin/FtsZ, GTPase domain / Tubulin-tyrosine ligase/Tubulin polyglutamylase / Tubulin-tyrosine ligase family / TTL domain profile. / Stathmin family / Stathmin, conserved site / Stathmin superfamily / Stathmin family / Stathmin family signature 1. / Stathmin family signature 2. / Stathmin-like (SLD) domain profile. / 60s Ribosomal Protein L30; Chain: A; / Alpha tubulin / Tubulin-beta mRNA autoregulation signal. / Beta tubulin, autoregulation binding site / Beta tubulin / Tubulin / Tubulin, C-terminal / Tubulin C-terminal domain / Tubulin, conserved site / Tubulin subunits alpha, beta, and gamma signature. / Tubulin/FtsZ family, C-terminal domain / Tubulin/FtsZ-like, C-terminal domain / Tubulin/FtsZ, C-terminal / Tubulin/FtsZ, 2-layer sandwich domain / Tubulin/FtsZ family, GTPase domain / Tubulin/FtsZ family, GTPase domain / Tubulin/FtsZ, GTPase domain / Tubulin/FtsZ, GTPase domain superfamily / Helix non-globular / Special / Helix Hairpins / Rossmann fold / 2-Layer Sandwich / Orthogonal Bundle / 3-Layer(aba) Sandwich / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
GUANOSINE-5'-DIPHOSPHATE / GUANOSINE-5'-TRIPHOSPHATE / Chem-O91 / Tubulin beta chain / Tubulin tyrosine ligase / Tubulin beta chain / Tubulin alpha-1B chain / Stathmin-4
Similarity search - Component
Biological speciesHomo sapiens (human)
Gallus gallus (chicken)
Sus scrofa (pig)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.602 Å
AuthorsKumar, G. / Wang, Y. / Li, W. / White, S.W.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Cancer Institute (NIH/NCI)R01CA148706 United States
CitationJournal: J.Med.Chem. / Year: 2020
Title: Structure-Activity Relationship Study of Novel 6-Aryl-2-benzoyl-pyridines as Tubulin Polymerization Inhibitors with Potent Antiproliferative Properties.
Authors: Chen, H. / Deng, S. / Wang, Y. / Albadari, N. / Kumar, G. / Ma, D. / Li, W. / White, S.W. / Miller, D.D. / Li, W.
History
DepositionJun 15, 2019Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 22, 2020Provider: repository / Type: Initial release
Revision 1.1Mar 13, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_struct_conn_angle / struct_conn / struct_ncs_dom_lim
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_auth_comp_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr2_label_atom_id / _pdbx_struct_conn_angle.ptnr2_label_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Tubulin alpha-1B chain
B: Tubulin beta-2B chain
C: Tubulin alpha-1B chain
D: Tubulin beta-2B chain
E: Stathmin-4
F: Tubulin Tyrosine Ligase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)264,48619
Polymers261,3056
Non-polymers3,18113
Water7,278404
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: assay for oligomerization
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)105.143, 157.533, 181.961
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11chain A
21(chain C and (resid 1 through 437 or resid 501 through 502))
12(chain B and (resid 2 through 273 or resid 284 through 428))
22(chain D and resid 2 through 428)

NCS domain segments:
Dom-IDComponent-IDEns-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
111METMETVALVALchain AAA1 - 4371 - 437
211METMETVALVAL(chain C and (resid 1 through 437 or resid 501 through 502))CC1 - 4371 - 437
221GTPGTPMGMG(chain C and (resid 1 through 437 or resid 501 through 502))CO - P501 - 502
112ARGARGLEULEU(chain B and (resid 2 through 273 or resid 284 through 428))BB2 - 2732 - 273
122LEULEUALAALA(chain B and (resid 2 through 273 or resid 284 through 428))BB284 - 428284 - 428
212ARGARGALAALA(chain D and resid 2 through 428)DD2 - 4282 - 428

NCS ensembles :
ID
1
2

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Components

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Protein , 4 types, 6 molecules ACBDEF

#1: Protein Tubulin alpha-1B chain / Alpha-tubulin ubiquitous / Tubulin K-alpha-1 / Tubulin alpha-ubiquitous chain


Mass: 50041.273 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Sus scrofa (pig) / References: UniProt: Q2XVP4
#2: Protein Tubulin beta-2B chain


Mass: 49999.887 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Sus scrofa (pig) / References: UniProt: A0A287AGU7, UniProt: P02554*PLUS
#3: Protein Stathmin-4 / Stathmin-like protein B3 / RB3


Mass: 16844.162 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: STMN4 / Production host: Escherichia coli (E. coli) / References: UniProt: Q9H169
#4: Protein Tubulin Tyrosine Ligase


Mass: 44378.496 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Gallus gallus (chicken) / Gene: TTL / Production host: Escherichia coli (E. coli) / References: UniProt: E1BQ43

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Non-polymers , 7 types, 417 molecules

#5: Chemical ChemComp-GTP / GUANOSINE-5'-TRIPHOSPHATE


Mass: 523.180 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H16N5O14P3 / Comment: GTP, energy-carrying molecule*YM
#6: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Mg
#7: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Ca
#8: Chemical ChemComp-GDP / GUANOSINE-5'-DIPHOSPHATE


Type: RNA linking / Mass: 443.201 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H15N5O11P2 / Comment: GDP, energy-carrying molecule*YM
#9: Chemical ChemComp-MES / 2-(N-MORPHOLINO)-ETHANESULFONIC ACID


Mass: 195.237 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C6H13NO4S / Comment: pH buffer*YM
#10: Chemical ChemComp-O91 / [2-(4-methylphenyl)-1H-imidazol-4-yl](3,4,5-trimethoxyphenyl)methanone


Mass: 352.384 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C20H20N2O4 / Feature type: SUBJECT OF INVESTIGATION
#11: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 404 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestY

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.88 Å3/Da / Density % sol: 57.34 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6.7
Details: 6% PEG 4000, 5% Glycerol, 0.1 M MES, 30 mM CaCl2, 30 mM MgCl2

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL19U1 / Wavelength: 0.97853 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Dec 10, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97853 Å / Relative weight: 1
ReflectionResolution: 2.6→50 Å / Num. obs: 93033 / % possible obs: 99.7 % / Redundancy: 6.6 % / Biso Wilson estimate: 43.49 Å2 / Rmerge(I) obs: 0.135 / Rpim(I) all: 0.057 / Rrim(I) all: 0.147 / Χ2: 0.958 / Net I/σ(I): 4.2 / Num. measured all: 609670
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
2.6-2.646.50.88845960.6810.3710.9640.96599.8
2.64-2.696.50.82345840.7170.3440.8940.97599.7
2.69-2.746.60.73345760.7680.3050.7950.99399.8
2.74-2.86.50.65146280.8020.2720.7071.00799.6
2.8-2.866.50.55446050.8490.2320.6021.00699.8
2.86-2.936.60.4946150.8790.2050.5320.989100
2.93-36.50.40646230.9160.1710.4420.99699.9
3-3.086.50.34746160.9370.1460.3771.01899.9
3.08-3.176.30.28245630.9480.1220.3080.99199.4
3.17-3.285.70.23846280.9520.110.2630.99999.2
3.28-3.396.80.20546320.9780.0840.2220.986100
3.39-3.5370.16346180.9850.0660.1771.019100
3.53-3.696.90.13846520.9880.0560.1491.026100
3.69-3.886.90.11146740.9920.0450.121.032100
3.88-4.136.80.0946460.9940.0370.0970.985100
4.13-4.456.60.07446980.9960.0310.080.922100
4.45-4.895.90.06146420.9950.0270.0670.87898.9
4.89-5.670.06947450.9960.0280.0740.853100
5.6-7.056.80.07147610.9950.0290.0760.823100
7.05-506.20.04349310.9980.0190.0470.71298.9

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassification
HKL-2000data scaling
PHASERphasing
PHENIXrefinement
PDB_EXTRACT3.25data extraction
HKL-2000data reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.602→41.742 Å / SU ML: 0.34 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 24.14
RfactorNum. reflection% reflection
Rfree0.2335 4594 4.99 %
Rwork0.1898 --
obs0.1919 92094 98.75 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 163.29 Å2 / Biso mean: 51.435 Å2 / Biso min: 17.65 Å2
Refinement stepCycle: final / Resolution: 2.602→41.742 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms17137 0 201 404 17742
Biso mean--40.53 46.12 -
Num. residues----2178
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDRmsType
11A2686X-RAY DIFFRACTION8.925TORSIONAL
12C2686X-RAY DIFFRACTION8.925TORSIONAL
21B2530X-RAY DIFFRACTION8.925TORSIONAL
22D2530X-RAY DIFFRACTION8.925TORSIONAL
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 30

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.6018-2.63140.29241300.26672598272888
2.6314-2.66230.29451520.26882685283793
2.6623-2.69480.36221400.26532796293696
2.6948-2.72890.34451500.25962816296697
2.7289-2.76480.3321590.25282968312799
2.7648-2.80270.3031450.25372840298599
2.8027-2.84270.30841660.24332877304399
2.8427-2.88510.33791420.234829183060100
2.8851-2.93020.28271500.236729273077100
2.9302-2.97820.30351530.23329193072100
2.9782-3.02960.28411470.22129403087100
3.0296-3.08460.26641620.218529183080100
3.0846-3.1440.27371290.218329273056100
3.144-3.20810.26641360.22329663102100
3.2081-3.27780.2761570.22382892304999
3.2778-3.35410.23751460.209229173063100
3.3541-3.43790.25861520.200329393091100
3.4379-3.53080.26251340.186629643098100
3.5308-3.63460.21341620.184129613123100
3.6346-3.75190.19951500.178229863136100
3.7519-3.88590.19851430.169229143057100
3.8859-4.04140.21321650.165629813146100
4.0414-4.22510.22921460.160729243070100
4.2251-4.44760.19861570.150129623119100
4.4476-4.72590.18841740.14072919309399
4.7259-5.09020.18311720.15242925309799
5.0902-5.60140.21911780.172230143192100
5.6014-6.40940.22681740.191929713145100
6.4094-8.06570.19751670.185530363203100
8.0657-41.74720.191560.16983100325697
Refinement TLS params.Method: refined / Origin x: 17.3001 Å / Origin y: -44.1771 Å / Origin z: -26.0829 Å
111213212223313233
T0.1358 Å2-0.015 Å2-0.0095 Å2-0.2478 Å2-0.0222 Å2--0.2744 Å2
L0.1301 °20.0333 °20.1176 °2-0.6007 °20.5359 °2--0.9323 °2
S-0.029 Å °-0.0163 Å °-0.0131 Å °-0.0151 Å °0.0794 Å °-0.0272 Å °-0.0265 Å °0.051 Å °-0.0401 Å °
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1allA1 - 437
2X-RAY DIFFRACTION1allA501 - 502
3X-RAY DIFFRACTION1allB2 - 428
4X-RAY DIFFRACTION1allB501 - 502
5X-RAY DIFFRACTION1allC1 - 440
6X-RAY DIFFRACTION1allC501 - 502
7X-RAY DIFFRACTION1allD1 - 431
8X-RAY DIFFRACTION1allE6 - 141
9X-RAY DIFFRACTION1allF1 - 380
10X-RAY DIFFRACTION1allL1
11X-RAY DIFFRACTION1allM11 - 12
12X-RAY DIFFRACTION1allN1 - 2
13X-RAY DIFFRACTION1allW1 - 410
14X-RAY DIFFRACTION1allK1 - 2

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